Does one of the amounts tie up with the app's price (plus your state's sales tax if you are in the US, with the other one being how much, and where are you seeing them (on emailed receipts, on your account's purchase history, on your credit card) ?
Did you add or change your credit card details on your iTunes account when making the purchase - each time that you do so a small temporary store holding charge ($1 or approximate local equivalent) may be applied to check that the card details are correct and valid and that it's registered to exactly the same name and address as on your iTunes account (it should disappear off your account within a few days or so). Store holding charge : http://support.apple.com/kb/HT3702
If you have got 2 actual charges on your iTunes account for buying the app then try the 'report a problem' page to contact iTunes Support : http://reportaproblem.apple.com
If the 'report a problem' link doesn't work then you can try contacting iTunes support via this page : http://www.apple.com/support/itunes/contact/- click on Contact iTunes Store Support on the right-hand side of the page, then Purchases, Billing & Redemption